Special Issue "Genomics of Giant Viruses"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Viruses of Plants, Fungi and Protozoa".

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editors

Prof. Philippe Colson
E-Mail
Guest Editor
IHU Méditerranée Infection, Microbes Evolution Phylogeny and Infections (MEPHI), IRD, Aix-Marseille Université, Assistance Publique-Hôpitaux de Marseille, Marseille, France
Interests: hepatitis viruses; HIV; epidemiological surveillance of infections; emerging viruses; genomics of giant viruses; interactions of plant viruses with humans
Prof. Dr. Jônatas Abrahão
E-Mail Website
Guest Editor
Department of Microbiology, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MT 31270-901, Brazil
Interests: giant viruses; large viruses; evolution; host–virus interactions
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The giant viruses discovered in 2003 have since been shown to be common in our biosphere. Their genetic diversity has expanded considerably, and sequences closest to those of giant viruses are frequently and sometimes abundantly found in metagenomes, potentially leading to the assembly of complete genomes. However, some isolated giant viruses have a genome sufficiently divergent to escape such detections based on similarity searches. This suggests that knowledge on the diversity of giant viruses is still rather incomplete. Analyses of the genomes of giant viruses revealed a complexity similar to that of small cellular organisms, with characteristics that distinguish them from classical viruses, including genes that are hallmarks of cellular organisms. In addition, they demonstrate the significant mosaicism of these genomes resulting from numerous transfers of sequences and integration events as well as considerable proportions of ORFans. These various features make the genomics of giant viruses, that we are addressing in this Special Issue, a hot topic in the field of evolutionary biology.

Prof. Philippe Colson
Prof. Dr. Jônatas Abrahão
Guest Editors

Manuscript Submission Information

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Keywords

  • giant virus
  • mimivirus
  • genomes
  • lateral sequence transfers
  • mosaicism
  • ORFans
  • evolution
  • classification

Published Papers (1 paper)

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Research

Article
ViralRecall—A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in ‘Omic Data
Viruses 2021, 13(2), 150; https://0-doi-org.brum.beds.ac.uk/10.3390/v13020150 - 20 Jan 2021
Cited by 3 | Viewed by 1233
Abstract
Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs [...] Read more.
Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in ‘omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall. Full article
(This article belongs to the Special Issue Genomics of Giant Viruses)
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